Daily Telegraph
Commander Jeremy Woods was sacked from the Type 22 frigate following "administrative action" taken by the Navy, the Ministry of Defence said.
But the Navy insisted that the dismissal was "absolutely not" related to the capture of 15 sailors and Royal Marines last year or to any personnel issues on board.
Although the Cornwall incident happened in March last year, Navy chiefs decided that Cdr Woods, 41, was not suitable to continue running the £250 million ship 16 months after the incident that caused national humiliation.
A Navy spokesman confirmed the officer had been "removed from command".
"This is an internal administrative matter between the individual and his senior officers and we will not give further details of the removal," he added.
He will remain in the Navy but is now likely to take up an administrative post "where his talent and experience can be used to best effect".
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"As a result of the Cornwall incident the Navy is getting pretty ruthless and if you are not up to scratch there is no way of hiding it these days," a serving officer said.
"If you cannot hack it you are shipped out because you cannot afford to risk one her Majesty's ships. There are also few ships around and plenty of young officers who want to command them."